SMTL ID : 1z7z.2 (3 other biounits)

Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 8.00 Å

Oligo State

hetero-5-5-5-5-5-mer

Ligands

5 x LEU- ILE- GLY- ARG- THR: human coxsackievirus A21(Non-covalent)

LEU-ILE-GLY-ARG-THR.1: 10 residues within 4Å: Chain A: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 Chain W: S.233, K.234 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.84 Hydrogen bonds: A:S.86, A:S.86, A:T.88, A:T.88, A:K.98 LEU-ILE-GLY-ARG-THR.10: 10 residues within 4Å: Chain C: S.233, K.234 Chain F: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.84 Hydrogen bonds: F:S.86, F:S.86, F:T.88, F:T.88, F:K.98 LEU-ILE-GLY-ARG-THR.19: 10 residues within 4Å: Chain H: S.233, K.234 Chain K: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:I.84 Hydrogen bonds: K:S.86, K:S.86, K:T.88, K:T.88, K:K.98 LEU-ILE-GLY-ARG-THR.28: 10 residues within 4Å: Chain M: S.233, K.234 Chain P: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain P Hydrophobic interactions: P:I.84 Hydrogen bonds: P:S.86, P:S.86, P:T.88, P:T.88, P:K.98 LEU-ILE-GLY-ARG-THR.37: 10 residues within 4Å: Chain R: S.233, K.234 Chain U: I.84, S.86, L.87, T.88, K.97, K.98, F.100, N.101 6 PLIP interactions: 6 interactions with chain U Hydrophobic interactions: U:I.84 Hydrogen bonds: U:S.86, U:S.86, U:T.88, U:T.88, U:K.98

40 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.2: 3 residues within 4Å: Chain E: N.103, T.145, L.147 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain E: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain E: G.126, E.127, N.156 Ligand excluded by PLIP NAG.5: 7 residues within 4Å: Chain E: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.6 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain E: Y.83, W.84, T.85 Ligands: NAG.5 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain E: G.239, N.240 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain E: W.97, P.99, N.269 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain E: N.358 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain J: N.103, T.145, L.147 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain J: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain J: G.126, E.127, N.156 Ligand excluded by PLIP NAG.14: 7 residues within 4Å: Chain J: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.15 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain J: Y.83, W.84, T.85 Ligands: NAG.14 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain J: G.239, N.240 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain J: W.97, P.99, N.269 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain J: N.358 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain O: N.103, T.145, L.147 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain O: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain O: G.126, E.127, N.156 Ligand excluded by PLIP NAG.23: 7 residues within 4Å: Chain O: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.24 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain O: Y.83, W.84, T.85 Ligands: NAG.23 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain O: G.239, N.240 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain O: W.97, P.99, N.269 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain O: N.358 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain T: N.103, T.145, L.147 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain T: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain T: G.126, E.127, N.156 Ligand excluded by PLIP NAG.32: 7 residues within 4Å: Chain T: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.33 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain T: Y.83, W.84, T.85 Ligands: NAG.32 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain T: G.239, N.240 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain T: W.97, P.99, N.269 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain T: N.358 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain Y: N.103, T.145, L.147 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain Y: A.117, N.118, P.167, Q.168 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain Y: G.126, E.127, N.156 Ligand excluded by PLIP NAG.41: 7 residues within 4Å: Chain Y: T.85, P.86, E.87, F.173, E.174, N.175 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain Y: Y.83, W.84, T.85 Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain Y: G.239, N.240 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain Y: W.97, P.99, N.269 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain Y: N.358 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, C. et al., The crystal structure of coxsackievirus a21 and its interaction with icam-1. Structure (2005)

Release Date

2005-08-02

Peptides

human coxsackievirus A21: AFKPU
human coxsackievirus A21: BGLQV
human coxsackievirus A21: CHMRW
human coxsackievirus A21: DINSX
Intercellular adhesion molecule-1: EJOTY

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

F
1

K
1

P
1

U
1

B
2

G
2

L
2

Q
2

V
2

C
3

H
3

M
3

R
3

W
3

D
4

I
4

N
4

S
4

X
4

E
I

J
I

O
I

T
I

Y
I

human coxsackievirus A21

human coxsackievirus A21

human coxsackievirus A21

human coxsackievirus A21

Intercellular adhesion molecule-1

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